How to bake normal map for discontinuous mesh
Here is a workflow you could use:


Build the high poly mesh first. 
Add details as you like by adding separate meshes.
Build the low poly mesh over high poly mesh, using Shrinkwrap and Surface Snapping to help.
Separate your low poly meshes according to requirements (textures, extrusion etc).
Bake your maps.


This ensures correct normal and AO map bakes.